Name	Short Description	Language
BLASTHits	Screen forward and reverse primer hits	Perl
BMTagger	Find host sequences with BMTagger (Rotmistrovsky and Agarwala, 2011) (Generated by PluGen)	C++
BMTool	Generate bitmask with BMTool (Rotmistrovsky and Agarwala, 2011) (Rotmistrovsky and Agarwala, 2011) (Generated by PluGen)	C++
CSVColumns	Extract columns of CSV file by name	Python
ChimeraRemove	Remove chimeric sequences	R
CSVChop	Return a range of rows from a CSV file	Python
CSVExtract	Extract rows from a CSV file with a specific value in a column	R
CSVFilter	Remove Columns from a CSV file with Zero Values above a threshold	Python
CSVIndex	Index a CSV file over a range of columns	Python
CSVNoDup	Remove duplicates from CSV file	Python
CSVNoUnderscore	Remove underscores from CSV file	Python
CSVRemove	Remove a column from a CSV file	Python
CSVRow	Extract rows from a CSV file	Python
CSVScarce	Remove scarce taxa	Python
CSVScreen	Remove all rows with a zero or non-zero value in a specific column	Python
CSVScreenTax	Remove all rows with a zero or non-zero abundance for a specific taxon (any phylogenetic tree level)	Python
CSVSelect	Select rows from CSV	Python
CSVTop	Obtain top abundant taxa	Python
CSVToss	Remove all observables that are not present in a threshold percentage of samples	Python
CSVTrim	Trim a CSV file to a specific set of columns	R
CSVUnique	Unique CSV entries	Python
CSVUpperTriangular	Upper triangular portion of a matrix	Python
Cut	Cut file based on delimiter	C++
Dereplication	Convert redundant reads into sequences and counts	R
Distribution	Filter by distribution	R
ExpressionFilter	Filter by expression level	R
Extract	Extract sequences that include a target sequence	Perl
FAAOrthologScreen	Screen two FASTA files for mutual orthologs	Python
FAIDX	Filter a FASTA file by sequence length range (Shirley et al, 2015) (Generated by PluGen)	C++
FASTAExtract	Extract a portion of a FASTA File	Python
FASTAUnique	Extract unique sequences from a FASTA file	C++
FASTQFilter	Filter a FASTQ file using a SAM alignment	Python
FileDump	Remove a set of files	C++
FilterAndTrim	Filter sequences for quality, and trim to a specified length	R
FilterNonExpressed	Remove non-expressed genes	R
FiltLong	FiltLong filter for long reads	C++
FilterChromosomes	Extract chromosome data from FASTA	Python
FilteringPTR	Taxa filter for Peak-To-Trough Ratio (PTR) analysis	Python
FilterLowQualityCells	Filter low-quality single cell data	R
FilterMicrobes	Filter out connections between metagenomic data based on underlying metabolic networks	Python
FilterPathway	Take a CSV and find all pathways present in PathwayTools (Karp et al, 2015)	Python
Host	Retrieve host sequences (Uritsky et al, 2018)	Python
IdentifyBacteria	Identify bacteria (query NCBI)	Perl
KronaClean	Clean a Krona file	Python
KronaIgnore	Ignore all taxa in Krona file that contain a specific string	Python
KronaNoGroups	Remove groups from a Krona file	Python
KronaNoVirus	Remove viruses from a Krona file	Python
Leek	Leek's Method (Leek et al, 2014)	R
LEfSeOnlyLowest	Restrict LEfSe (Segata et al, 2011) output to lowest taxonomic level	Python
LEfSeRemoveZero	Convert LEfSe (Segata et al, 2011) output to biomarkers only (nonzero LDA score)	Python
MicrobeOutput	Extract microbial output	R
MicrobeReads	Extra microbial reads	R
Microbial	Retrieve microbial sequences (Uritsky et al, 2018)	Python
MinExpress	Filter by minimum expression level	R
MothurFilter	Filter Mothur (Schloss et al, 2009) taxa	Python
MultiomicScreen	Screen taxa correlations, leaving only heterogeneous	Python
NFilter	Filter out sequences with too many N's (uncertain)	Python
PathwayFilter	Take a CSV and remove all connections with no corresponding pathway in PathwayTools (Karp et al, 2015)	Python
PhyloSeqExtract	Extract samples of a specific category from PhyloSeq (McMurdie et al, 2013) data	R
PhyloSeqExtractTwo	Extract two categories from PhyloSeq data (McMurdie et al, 2013)	R
PhyloSeqFilter	Filter PhyloSeq (McMurdie and Holmes, 2013) data	Python
PhyloSeqGlom	Collect PhyloSeq (McMurdie et al, 2013) at a specific taxonomic level	R
PhyloSeqRemove	Filter PhyloSeq (McMurdie et al, 2013) data	R
ProcessDesc	Extract phylogenetic information from FASTA file	Perl
PruneInternals	Prune internal nodes of phylogenetic tree	Python
Qiime2Filter	Filter Qiime2 (Bolyen et al, 2019) reads based on a feature	C++
Rarefy	Rarefying, ad hoc (McMurdie and Holmes, 2014)	R
RemoveNegative	Remove negative edges	Python
RemoveRow	Remove a row of a file	Python
RemoveSingletons	Remove singleton taxa	Python
RemoveTaxa	Remove taxa with a certain property	Python
RemoveUnclassified	Remove unclassified taxa	Python
RemoveZero	Remove zero-abundant entities	Python
SelectGeneFamilies	Gene families	Python
SelectTIM	Samples with Ticarcillin-clavulonic acid (TIM)	Python
Subset	Obtain a subset of PhyloSeq (McMurdie and Holmes, 2013) data	R
Subspecies	Obtain subspecies from a KRONA file	Python
TaxaPrune	Prune PhyloSeq (McMurdie and Holmes, 2013) taxa	Python
Threshold	Remove all observables from a dataset with a low frequency of occurrence	R
TSVColumns	Select a set of columns from a TSV file	Python
TSVFilter	Remove Columns from a TSV file with Zero Values above a threshold	Python
UnionSelect	Union of selected elements from two datasets	Python
Unique	Output unique genes	R
UniqueGroups	Output the unique groups	Python
UniqueSequences	Output all unique sequences in a FASTA file	Python

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